Gene Expression Profiling of Functional Murine Embryonic Stem Cell-Derived Cardiomyocytes and Comparison with Adult Heart: Profiling of Murine ESC-Derived Cardiomyocytes

Although embryonic stem cell (ESC)—derived cardiomyocytes may be a powerful tool in drug discovery, their potential has not yet been fully explored. Nor has a detailed comparison with adult heart tissue been performed. We have developed a method for efficient production of cardiomyocyte-rich embryoid bodies (EBs) from murine ESCs. Analysis of global gene expression profiles showed that EBs on day 7 and/or 21 of differentiation (d7CMs and d21CMs, respectively) were similar to adult heart tissue for genes categorized as regulators of muscle contraction or voltage-gated ion channel activity, although d21CMs were more mature than d7CMs for contractile components related to morphological structures. Calcium and sodium channel blockers altered Ca2+ transients, and isoproterenol, a β-adrenergic compound, increased the rate of beating in d7CMs and d21CMs. Our gene analytic system therefore enabled us to identify genes that are expressed in the physiological pathways associated with ion channels and structural components in d7CMs and d21CMs. We conclude that EBs might be of use for the basic screening of drugs that might affect contractile function through ion channels. ( Journal of Biomolecular Screening 2009:239-245)

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Global transcriptional profiling reveals similarities and differences between human stem cell-derived cardiomyocyte clusters and heart tissue

Physiological Genomics ◽

10.1152/physiolgenomics.00118.2011 ◽

2012 ◽

Vol 44 (4) ◽

pp. 245-258 ◽

Cited By ~ 50

Author(s):

Jane Synnergren ◽

Caroline Améen ◽

Andreas Jansson ◽

Peter Sartipy

Keyword(s):

Stem Cell ◽

Ion Channels ◽

Human Heart ◽

Embryonic Stem ◽

Heart Tissue ◽

Phenotypic Characterization ◽

Adult Heart ◽

Promising Source

It is now well documented that human embryonic stem cells (hESCs) can differentiate into functional cardiomyocytes. These cells constitute a promising source of material for use in drug development, toxicity testing, and regenerative medicine. To assess their utility as replacement or complement to existing models, extensive phenotypic characterization of the cells is required. In the present study, we used microarrays and analyzed the global transcription of hESC-derived cardiomyocyte clusters (CMCs) and determined similarities as well as differences compared with reference samples from fetal and adult heart tissue. In addition, we performed a focused analysis of the expression of cardiac ion channels and genes involved in the Ca2+-handling machinery, which in previous studies have been shown to be immature in stem cell-derived cardiomyocytes. Our results show that hESC-derived CMCs, on a global level, have a highly similar gene expression profile compared with human heart tissue, and their transcriptional phenotype was more similar to fetal than to adult heart. Despite the high similarity to heart tissue, a number of significantly differentially expressed genes were identified, providing some clues toward understanding the molecular difference between in vivo sourced tissue and stem cell derivatives generated in vitro. Interestingly, some of the cardiac-related ion channels and Ca2+-handling genes showed differential expression between the CMCs and heart tissues. These genes may represent candidates for future genetic engineering to create hESC-derived CMCs that better mimic the phenotype of the cardiomyocytes present in the adult human heart.

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Correlation of Murine Embryonic Stem Cell Gene Expression Profiles with Functional Measures of Pluripotency

Stem Cells ◽

10.1634/stemcells.2004-0157 ◽

2005 ◽

Vol 23 (5) ◽

pp. 663-680 ◽

Cited By ~ 106

Author(s):

Lars Palmqvist ◽

Clive H. Glover ◽

Lien Hsu ◽

Min Lu ◽

Bolette Bossen ◽

...

Keyword(s):

Gene Expression ◽

Stem Cell ◽

Embryonic Stem Cell ◽

Expression Profiles ◽

Embryonic Stem ◽

Gene Expression Profiles ◽

Murine Embryonic Stem Cell ◽

Cell Gene Expression ◽

Cell Gene ◽

Stem Cell Gene

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Optimization of the TeraTox assay for preclinical teratogenicity assessment

10.1101/2021.07.06.451364 ◽

2021 ◽

Author(s):

Manuela Jaklin ◽

Jitao David Zhang ◽

Nicole Schaefer ◽

Nicole Clemann ◽

Paul Barrow ◽

...

Keyword(s):

Gene Expression ◽

Machine Learning ◽

Stem Cell ◽

Expression Profiles ◽

Embryonic Stem ◽

Mouse Embryonic Stem Cell ◽

Embryoid Bodies ◽

Cell Renewal ◽

Germ Layer

Teratogenicity poses severe threats to patient safety. Stem-cell-based in vitro systems are promising tools to predict human teratogenicity. However, current in vitro assays are limited because they either capture effects on a certain germ layer, or focus on a subset of predictive markers. Here we report the characterization and critical assessment of TeraTox, a newly developed multi-lineage differentiation assay using 3D human induced pluripotent stem cells. TeraTox probes stem-cell derived embryoid bodies with two endpoints, one quantifying cytotoxicity and the other inferring the teratogenicity potential with gene expression as a molecular phenotypic readout. To derive teratogenicity potentials from gene expression profiles, we applied both unsupervised machine-learning tools including factor analysis and supervised tools including classification and regression. To identify the best predictive model for the teratogenicity potential that is explainable, we systematically tested 64 machine-learning model architectures and identified the optimal model, which uses expression of 77 representative germ-layer genes, summarized by 10 latent germ-layer factors, as input for random-forest regression. We combined measured cytotoxicity and inferred teratogenicity potential to predict concentration-dependent teratogenicity profiles of 33 approved pharmaceuticals and 12 proprietary drug candidates with known in vivo data. Compared with the mouse embryonic stem cell test, which has been in routine use for more than a decade, the TeraTox assay shows higher sensitivity, particularly towards teratogens impairing ectodermal development or stem-cell renewal, and a more balanced prediction performance. We envision that further refinement and development of TeraTox has the potential to reduce and replace animal research in drug discovery and to improve preclinical assessment of teratogenicity.

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Gene Expression Profiles of Similarly Derived Human Embryonic Stem Cell Lines Correlate with Their Distinct Propensity to Exit Stemness and Their Different Differentiation Behavior in Culture

Cellular Reprogramming ◽

10.1089/cell.2013.0089 ◽

2014 ◽

Vol 16 (3) ◽

pp. 185-195 ◽

Cited By ~ 2

Author(s):

Oliver Sterthaus ◽

Anne-Catherine Feutz ◽

Hong Zhang ◽

Flurina Pletscher ◽

Elisabeth Bruder ◽

...

Keyword(s):

Gene Expression ◽

Stem Cell ◽

Embryonic Stem Cell ◽

Cell Lines ◽

Human Embryonic Stem Cell ◽

Expression Profiles ◽

Embryonic Stem ◽

Gene Expression Profiles ◽

Stem Cell Lines

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Identification of molecules derived from human fibroblast feeder cells that support the proliferation of human embryonic stem cells

Cellular & Molecular Biology Letters ◽

10.2478/s11658-010-0039-8 ◽

2011 ◽

Vol 16 (1) ◽

Cited By ~ 13

Author(s):

Sergey Anisimov ◽

Nicolaj Christophersen ◽

Ana Correia ◽

Vanessa Hall ◽

Ingrid Sandelin ◽

...

Keyword(s):

Gene Expression ◽

Stem Cell ◽

Embryonic Stem Cell ◽

Human Embryonic Stem Cell ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Embryonic Stem ◽

Feeder Cells ◽

Continuous Growth

AbstractThe majority of human embryonic stem cell lines depend on a feeder cell layer for continuous growth in vitro, so that they can remain in an undifferentiated state. Limited knowledge is available concerning the molecular mechanisms that underlie the capacity of feeder cells to support both the proliferation and pluripotency of these cells. Importantly, feeder cells generally lose their capacity to support human embryonic stem cell proliferation in vitro following long-term culture. In this study, we performed large-scale gene expression profiles of human foreskin fibroblasts during early, intermediate and late passages using a custom DNA microarray platform (NeuroStem 2.0 Chip). The microarray data was validated using RT-PCR and virtual SAGE analysis. Our comparative gene expression study identified a limited number of molecular targets potentially involved in the ability of human neonatal foreskin fibroblasts to serve as feeder cells for human embryonic stem cell cultures. Among these, the C-KIT, leptin and pigment epithelium-derived factor (PEDF) genes were the most interesting candidates.

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